What, where and weather? Integrating open-source taxonomic, spatial and climatologic information into a comprehensive database of livestock infections

影响我们牲畜的病原体种类有哪些？回答这个问题很重要，这有助于保护生产我们食物的动物，也因为每10个人类病原体中就有近7个来自动物，其中很大一部分来自与我们密切相关的牲畜和宠物。然而，值得注意的是，即使对于人类，这个问题也只是在十年前才得到回答（列出了1415种），而对于牲畜，家养宠物和其他动物，仍然没有明确的答案。这项提案旨在进一步开发一个新的牲畜（和其他）病原体数据库，称为EID 2（ENHanCED Infectious Diseases 2）。EID 2主要是从上传到公共数据库的数千万条DNA和RNA序列记录中建立的;如果这些序列来自病原体，它们经常与宿主（病原体来自哪种动物），何时何地获得以及由谁获得的进一步信息一起上传。EID 2利用这些信息并得出结论;例如，某种类型的病原体感染了某种宿主物种，并且在某个时间存在于某个国家。从其他公共数据库中保存的数千万出版物中可以得出类似的结论，并将其添加到EID 2中，从而涵盖测序尚未广泛的时间和地点。EID 2可以绘制病原体的地图，并使用整合的气候数据，它可以模拟决定其分布的气候条件。EID 2是开放获取的。TRDF的资助将使我们能够完成EID 2的开发，使其成为牲畜和家养宠物病原体研究人员的工具和资源。我们将开发数据库，以保存更多的空间详细信息（在县而不是国家一级），并提高其处理宿主物种没有明确定义的记录的能力。我们将添加更多的环境数据，让用户能够制作更好的模型来解释病原体的分布，甚至在未来预测它们，考虑到气候变化;我们将允许用户在疾病层面上工作，而不是单个病原体或病原体组。最后，我们将允许用户添加自己的某些信息。

What are all the species of pathogen that affect our livestock? It is important to answer this question, to help protect the animals that produce our food, and also because nearly 7 out of every 10 human pathogens came from animals, with a good number from the livestock and pets that we closely associate with. Remarkably, however, even for humans this question was only answered ten years ago (1415 were listed) and there remains no definitive answer for livestock, domestic pets and other animals.This proposal aims to further develop a new database of livestock (and other) pathogens, called EID2 (ENHanCED Infectious Diseases 2). EID2 has been built largely from the tens of millions of records of DNA and RNA sequences that are uploaded onto public databases; where such sequences are from a pathogen, they are frequently uploaded with further information on the host (which animal the pathogen was obtained from), where and when it was obtained, and who by. EID2 takes this information, and draws conclusions; for example, that a certain type of pathogen infects a certain host species, and is/was present in a certain country at a certain time. Similar conclusions can be drawn, and added to EID2, from the tens of millions of publications held in other public databases, thereby covering times and places where sequencing has not been extensive. EID2 can map the pathogens and, using incorporated climate data, it can model the climate conditions that determine their distribution. EID2 is open access.TRDF funding will enable us to finalise the development of EID2 into a tool and resource for researchers of pathogens of livestock and domestic pets. We will develop the database to hold more spatially detailed information (at county rather than country level) and improve its ability to handle records where the host species is not clearly defined. We will add further environmental data to allow users to produce better models to explain pathogen distributions, and even predict them in the future, given climate change; and we will allow users to work at the level of diseases, rather than individual pathogens or groups of pathogens. Finally, we will give users the ability to add certain information of their own.